Three Different Endings

Confusion, terror, and overwhelming sorrow.

That was the majority's reaction to the laser-focused male human who showed up in front of them, a strange, black branch made from metal in his hands. This was quickly hidden by semi-realistic smiles and welcoming postures.

"H-h-ello! My name is Twilight Sparkle, and I would be glad to be the first to welcome you to Ponyville and Equestria!"

Glaring at her and her friends as they huddled together, he studied them critically while looking around at the semi destroyed Ponyville. Buildings were in states that ranged from ashes and complete collapse to newly rebuilt and painted. Ponies were gathering around the group from tent homes and rebuilt businesses, nervously wondering about this new arrival and whether he knew about Jason as whispers echoed throughout the gathering group.
As the minutes passed by with agonizing slowness, it slowly dawned on him that this wasn’t what he was expecting.

"T-thank you.’

He gulped while staring at the destroyed Sweet Apple Acres, the stick slowly wobbling as he shook his head, then refocused on the contrite, nervously waiting, and bravely standing mares.

'Um- is it safe to say that I took a wrong turn in that-? Oh, who am I kidding? I knew I shouldn't have clicked on that link…"

Looking around, he came to a conclusion that left Twilight, her friends, and the other ponies, gobsmacked.

"At least this Equestria isn't threatening my species with extinction…"

A heartbreaking and stunned silence collapsed on the two groups, leading Twilight to shake her head in disbelief, before choking back some sobs at her realization.

"I-I-I'm sorry, but did you say extinction?!"

He squatted, nodding gravely.

“It seems like you’ve gone through something yourself. Mind telling me what happened, Twilight? Or maybe I should ask Applejack. Rainbow?”

The whole group freezes, then releases their collective breath, Applejack choosing to speak.

“A-.”

A golden flash erupted next to them, the light revealing a fairly worried Princess Celestia. Sparing a quick and glad glance at her little ponies as they bowed, she refocused on the quickly standing human, noticing the weapon hanging on his shoulder being brought to bear against her, a mask of fury on his face.

"You're the one behind this and me being here, aren't you?! Punishing your fellow Princess, her friends, your subjects, and me for whatever sick reason-!"

Her mentor’s and fellow ponies' horrified expressions and tears caused him to closely examine them, take some calming breaths, and lower the weapon again.

“Forgive me, Your Majesty. I-. I come from a world where another you, and another version of these mares and the rest of your subjects and army, as well as the whole Crystal Empire, are trying to murder my species.”

Her face changed from horror to seriousness, her flowing tears continuing even as her mane and tail threatened to burst into flame, her teeth sharpening.

“Give me a little time, and you’ll have everything I can spare. Come with me to-.”

“Oh, I do believe that we have another visitor, do we not?”

With a weak series of snaps, a clearly injured Discord appeared in front of the group, a mask of mischievousness hiding a shattered heart. In response, Fluttershy stood up straight while hissing at him. Flattening her ears, she thrust her head forward, lifting her foreleg and pawing the ground with it, growling, “Say a single wrong word, and I will shatter every bucking bone in your lower body, followed by your feathering ribs, you rutting monster!!”

Releasing his mask as the rest of the gathered ponies vocally agreed with her, he lowered himself to the ground, on the verge of tears. Taking a deep and shaky breath, he attempted to communicate with the new human.

"I, I need to-."

Twilight savagely stuffed a hoof into his mouth, his teeth breaking as he desperately tried to speak.

"It's- It's nothing! I would like to get to know all the details about you and your situation after you and the Princess talk!"

Lifting an eyebrow at this while nodding at the purple Alicorn, the human shook his head while stepping closer to Celestia.

“I’m trusting you as the Co-Princess of Equestria, Your Highness.”

After nodding back, they disappeared as Discord began quietly sobbing and trembling. After Twilight slammed his head into the ground, she removed her hoof and wiped it clean on his body.

"P-P-please! I've done what I can to-!"

His own screams of pain interrupted him as Twilight hit him with a torturing magic spell, augmented by an enchanted medallion with lavender colored Chaos magic. It started as high as he could stand before it quickly dropped to a subtle current that continued to send painful shocks throughout his body.
As the ponies left the quietly moaning and twitching draconequus while occasionally slamming a hoof into his body, Fluttershy stayed behind to use her medallion to absorb part of his magic, cancel the spell, and heal him.

"Th-th-thank you for-."

Crack.

He was left in speechless horror and pain as she bucked him in the exact relative place, with the exact strength, Applejack did with Jason. Staring at him emotionlessly, she wiped away tears, steadied herself and galloped away, Rainbow having kept her distance.
Approaching him as he struggled to leave through a microscopic portal, she flipped him over with an unused and muscular wing. Gently laying a hoof on the top of his head, she traced a path down his forehead, over his right eye, and down his body, tapping the center of his groin to his confusion and slowly increasing terror. Tears freely flowing, she spoke as her medallion glowed with cyan colored Chaos magic.

"What you enabled me to do, I now do unto you."

A thunderous crack of rainbow lightning lanced its way down the path she traced, thankfully knocking him out before he suffered too much or even screamed. Setting her hoof on the ground, the medallion glowed, teleporting her to the castle as Discord's tears continued to flow, evaporating off of his sparking body.